Season two timeline discontinuity
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The first season of the Re-imagined Series of Battlestar Galactica kept track of the episode timeline meticulously, announcing the number of days since the Fall of the Twelve Colonies during the first scene on Cylon-occupied Caprica in each episode.
While this convention was abandoned during the second season, the timeline can still be established based on various date references scattered throughout episode dialogue. However, when the available information is compiled, it becomes clear that there is an discontinuity of approximately 75 days in the middle of season two.
There is a roughly 75 day discontinuity between Roslin's date of death as projected during the first half of the season (day 114, or at most a few weeks later) and the actual moment of her would-be-death (a few days after Day 189).
This discontinuity cannot be plausibly explained or "fanwanked". It is not simply a matter of Cottle's medical opinion being incorrect by a span of three months, since there are numerous other contradictions which arise from the error:
In short, it appears that the missing 75 days have not merely been glossed over, but were excised entirely. Valerii's pregnancy progresses by 75 days, but Roslin's cancer does not; elections are delayed by two months without explanation; and while all other references to the timeline have advanced by approximately two and a half months, no actual events during that span have been alluded to.
Some insight into the nature of the error is given in Ron Moore's podcast for for "Lay Down Your Burdens, Part I". Moore states that he believes/remembers that "Bastille Day" said that the elections were due "in nine months", even though the dialog in that episode actually said "seven months". It appears that Moore has simply forgotten the earlier episodes' statements.
Events of the first half of Season 2 can be dated with a good deal of certainty from the last episode of Season 1 as follows:
Scattered, Valley of Darkness, and Fragged
These three episodes clearly take place during the same day as the first season cliffhanger, "Kobol's Last Gleaming, Part II", which is explicitly stated to take place 51 days after the Cylon attack.
This episode begins with William Adama resuming command of Galactica. In the episode "Final Cut", D'anna Biers states that Saul Tigh was in command of Galactica for "over a week". The pragmatics of the phrase "over a week" imply at most a 10 day span, since 11 days is "almost two weeks", and absolutely rule out any time span longer than 13 days.
Thus, "The Farm" probably begins no later than day 61, and absolutely no later than day 64.
The majority of "Resistance" appears to cover a two-day period. At the beginning of the episode, Lee Adama asks Anastasia Dualla, "How's my father today?". The tone of their conversation implies that this is not the first time he's asked, as does Ronald D. Moore in his podcast:
Lee Adama's first opportunity to have this conversation would have been the morning of day 52. If this conversation has happened at least once already, that puts the earliest possible date for this episode at day 53.
A comparatively early date for this episode is also suggested by Tigh's interrogation of Chief Tyrol at the beginning of the episode, which cannot have taken place very long after his rescue from Kobol in the previous episode, at the end of day 51.
Another limit can be placed on this episode based on a scene cut from beginning of "The Farm" in which Roslin states that it's been an "entire week" since her escape, which takes place at the end of this episode. Since, as established above, "The Farm" cannot begin any later than day 64, "Resistance" cannot end any later than day 57.
Thus, the earliest (and most likely) dates for "Resistance" are days 53-54, with the latest possible dates being days 56-57.
Flight of the Phoenix
Cally is detained for "discharging a firearm without permission" and sentenced to thirty days in the brig on the evening of day 54. Cally is released at the beginning of "Flight of the Phoenix", dating the beginning of this episode to day 84.
In this episode Dr. Cottle updates Laura Roslin's prognosis, stating that she has one month to live, "at the outside". The actual date of this diagnosis is difficult to determine. Not much is accomplished on the Blackbird's construction during the time span, but it's likely that the Chief spent some time working up blueprints before beginning work. All that can be said with certainty is that Roslin's projected date of death is sometime after day 114, but apparently not more than a few weeks at most.
Following the mid-season break, it became apparent that a fairly large period of time could not be accounted for.
Resurrection Ship, Part I
In this episode, Helena Cain offhandedly asks "Is this what the two of you have been doing for the past six months? Debating the finer points of colonial law?"
President Roslin is transferred to Galactica at the beginning of this episode, which is explicitly stated to begin some 189 days after the Cylon attack. As her death draws nigh, Adama notes that she "has been aboard Galactica for the last few days".
An indication that a significant amount of time has passed since the "Resurrection Ship" episodes is made by Dr. Baltar, who tells his internal Six that "it was weeks ago," probably referring to his request that she leave him alone to work with the Pegasus Cylon prisoner. This can account for anything from 14 to 24 days--anything longer and he likely would have said "a month"--of the approximately 75 unaccounted for. Roslin's loss of function shown at the beginning of this episode is more believable given this timeframe.
The Captain's Hand
When asked to make a projection on the Fleet's population trend, Baltar states that he "made an initial calculation on these figures over seven months ago". We might speculate that this was done concurrently with the calculations he presented in "Water", putting this episode at roughly day 235, but in any case no earlier than day 225.
Lay Down Your Burdens, Part I
Tom Zarek comments that people of the Fleet have been "cooped up in metal boxes for nine months", putting this episode at roughly Day 270.